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| Status |
Public on Aug 22, 2018 |
| Title |
TPC1115_shPRMT2_1_RNAseq |
| Sample type |
SRA |
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| Source name |
TPC1115_shPRMT2_RNAseq
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| Organism |
Homo sapiens |
| Characteristics |
cell line: TPC1115
cell type: glioblastoma cells
transfected with: shPRMT2 lentivirus
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| Treatment protocol |
U87 cells were infected with shPRMT2 lentivirus
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| Growth protocol |
The glioblastoma cell lines U87 was cultured in DMEM containing 10% fetal bovine serum (FBS). TPC1115 was obtained from fresh surgical specimens of human primary GBMs and cultured as either monolayer or tumorspheres in DMEM/F12 medium supplemented with N2, B27 (Gibco), 20 ng/ml human Fibroblast Growth Factor-basic (bFGF, Sino Biological, Beijing, China), 20 ng/ml Epidermal Growth Factor-basic (EGF, Sino Biological, Beijing, China).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated using Trizol reagent (Ambion)
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
RNA-seq analysis was completed by BGI company(Shenzhen,China). For ChIP-seq, Clean reads were obtained from sequencing company.
Clean reads were aligned to human reference genome (hg19) using Bowtie2 version 2.2.9. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS version 1.4.2. and ChIPseeker package respectively.
Heatmaps and average profiles were generated by deepTools V2.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include FPKM values for each sample. For ChIP-seq, bigwig files were generated using deepTools V2.4.0, score represents the normalized coverage of DNA fragments at a given genomic coordinate.
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| Submission date |
Feb 09, 2018 |
| Last update date |
Aug 22, 2018 |
| Contact name |
xudong Wu |
| Organization name |
Tianjin medical university
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| Street address |
Qixiangtai Road
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| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE110424 |
PRMT2 links histone H3R8 asymmetric dimethylation to oncogenic activation and tumorigenesis of glioblastoma |
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| Relations |
| BioSample |
SAMN08513922 |
| SRA |
SRX3678219 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2991150_TPC1115_KD_1_FPKM.txt.gz |
126.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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